Variant report

Variant	rs73299518
Chromosome Location	chr12:50449518-50449519
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr12:50449465-50450201	HCT-116	colon:	n/a	chr12:50449936-50449955
2	MAX	chr12:50449488-50450216	A549	lung:	n/a	n/a
3	RAD21	chr12:50449212-50450384	SK-N-SH	brain:	n/a	chr12:50449346-50449353 chr12:50449936-50449955 chr12:50450313-50450320
4	CTCF	chr12:50449290-50450462	HCT-116	colon:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
5	CTCF	chr12:50449511-50450097	K562	blood:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
6	CEBPB	chr12:50449465-50449939	MCF-7	breast:	n/a	n/a
7	RAD21	chr12:50449460-50450177	SK-N-SH_RA	brain:	n/a	chr12:50449936-50449955
8	TAL1	chr12:50449463-50449625	K562	blood:	n/a	n/a
9	MAX	chr12:50449504-50450018	MCF-7	breast:	n/a	n/a
10	MAX	chr12:50449472-50450159	HepG2	liver:	n/a	n/a
11	RAD21	chr12:50449261-50450363	HCT-116	colon:	n/a	chr12:50449346-50449353 chr12:50449936-50449955 chr12:50450313-50450320
12	MAX	chr12:50449444-50450136	HepG2	liver:	n/a	n/a
13	MAX	chr12:50449381-50450532	A549	lung:	n/a	n/a
14	E2F6	chr12:50449490-50450058	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr12:50449460-50449610	GM12870	blood:	n/a	n/a
16	EGR1	chr12:50449446-50450005	MCF-7	breast:	n/a	chr12:50449673-50449682 chr12:50449672-50449685 chr12:50449672-50449685
17	RAD21	chr12:50449467-50450261	MCF-7	breast:	n/a	chr12:50449936-50449955
18	RAD21	chr12:50449461-50450279	A549	lung:	n/a	chr12:50449936-50449955
19	USF1	chr12:50449444-50449987	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr12:50449454-50450235	ECC-1	luminal epithelium:	n/a	n/a
21	MAX	chr12:50449274-50450212	HCT-116	colon:	n/a	n/a
22	NR2F2	chr12:50449240-50450032	K562	blood:	n/a	n/a
23	E2F6	chr12:50449365-50450165	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr12:50449480-50449630	GM12874	blood:	n/a	n/a
25	MXI1	chr12:50449506-50452883	SK-N-SH	brain:	n/a	n/a
26	SMC3	chr12:50449323-50451865	SK-N-SH	brain:	n/a	chr12:50449940-50449954
27	MAX	chr12:50449472-50450099	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr12:50449287-50452309	SK-N-SH	brain:	n/a	chr12:50449938-50449956 chr12:50451041-50451050 chr12:50451664-50451677 chr12:50449933-50449954 chr12:50451252-50451265 chr12:50451667-50451680 chr12:50451391-50451404 chr12:50451060-50451073
29	YY1	chr12:50449418-50450032	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr12:50449434-50450203	MCF-7	breast:	n/a	n/a
31	ZNF263	chr12:50449463-50451684	HEK293-T-REx	kidney:	n/a	chr12:50450637-50450646 chr12:50450344-50450353
32	MAX	chr12:50449440-50450182	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr12:50449504-50450132	K562	blood:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
34	RAD21	chr12:50449465-50450263	H1-hESC	embryonic stem cell:	n/a	chr12:50449936-50449955
35	MAX	chr12:50449377-50450258	HCT-116	colon:	n/a	n/a
36	CTCF	chr12:50449420-50449570	SAEC	small airway:	n/a	n/a
37	CTCF	chr12:50449420-50449570	GM12871	blood:	n/a	n/a
38	MAZ	chr12:50449258-50450248	IMR90	lung:	n/a	n/a
39	E2F6	chr12:50449476-50450061	A549	lung:	n/a	n/a
40	MAX	chr12:50449445-50450106	K562	blood:	n/a	n/a
41	ZNF143	chr12:50449496-50450191	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAX	chr12:50449434-50450189	ECC-1	luminal epithelium:	n/a	n/a
43	CTCF	chr12:50449411-50450282	MCF-7	breast:	n/a	chr12:50449938-50449956 chr12:50449933-50449954

No.	Distal block	Cell Line	Cell type
1	chr12:50432725..50434312-chr12:50449330..50450437,10	MCF-7	breast:
2	chr12:50368102..50368945-chr12:50449516..50450250,3	K562	blood:
3	chr12:50415480..50421111-chr12:50448192..50451032,5	K562	blood:
4	chr12:50358701..50362803-chr12:50449341..50451682,4	MCF-7	breast:
5	chr12:50369533..50370611-chr12:50449444..50450226,3	MCF-7	breast:
6	chr12:50415480..50418292-chr12:50448192..50450079,2	K562	blood:
7	chr12:50367707..50368705-chr12:50449431..50450774,7	MCF-7	breast:
8	chr12:50360514..50361964-chr12:50449435..50451127,13	K562	blood:
9	chr12:50360496..50362709-chr12:50448964..50450845,14	MCF-7	breast:
10	chr12:50432739..50435190-chr12:50449417..50450489,14	K562	blood:
11	chr12:50347500..50349334-chr12:50448823..50450713,2	MCF-7	breast:

Variant related genes	Relation type
ASIC1	TF binding region
ENSG00000086159	Chromatin interaction
ENSG00000161800	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10875995	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169263	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11169270	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376184	0.82[EUR][1000 genomes]
rs56990521	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs590460	0.89[EUR][1000 genomes]
rs685012	0.91[EUR][1000 genomes]
rs706794	0.84[EUR][1000 genomes]
rs73299515	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956491	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964698	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50444400-50449600	Weak transcription	Brain Angular Gyrus	brain
2	chr12:50444400-50449600	Weak transcription	Gastric	stomach
3	chr12:50444400-50449600	Weak transcription	Spleen	Spleen
4	chr12:50444400-50450800	Weak transcription	Lung	lung
5	chr12:50444600-50449600	Weak transcription	Brain Hippocampus Middle	brain
6	chr12:50444600-50449600	Weak transcription	Brain Substantia Nigra	brain
7	chr12:50444600-50449600	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:50444600-50449600	Weak transcription	Pancreas	Pancrea
9	chr12:50444800-50450800	Weak transcription	Right Atrium	heart
10	chr12:50445200-50449600	Weak transcription	Ovary	ovary
11	chr12:50445400-50449600	Weak transcription	Right Ventricle	heart
12	chr12:50445400-50450000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:50445800-50449600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:50447400-50449600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:50447600-50449600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:50448000-50449600	Weak transcription	Fetal Heart	heart
17	chr12:50449400-50449600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
18	chr12:50449400-50449600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
19	chr12:50449400-50449600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
20	chr12:50449400-50449600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
21	chr12:50449400-50449600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:50449400-50449600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:50449400-50449600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:50449400-50449600	Enhancers	Brain Anterior Caudate	brain
25	chr12:50449400-50449600	Enhancers	Brain Germinal Matrix	brain
26	chr12:50449400-50449600	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr12:50449400-50449600	Enhancers	Fetal Brain Female	brain
28	chr12:50449400-50449600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
29	chr12:50449400-50449600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
30	chr12:50449400-50449600	Enhancers	A549	lung
31	chr12:50449400-50449600	Enhancers	Hela-S3	cervix
32	chr12:50449400-50449600	Enhancers	K562	blood
33	chr12:50449400-50449600	Enhancers	NHEK	skin
34	chr12:50449400-50449800	Bivalent Enhancer	Fetal Kidney	kidney
35	chr12:50449400-50450000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:50449400-50450600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr12:50449400-50450600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr12:50449400-50450600	Enhancers	Fetal Brain Male	brain
39	chr12:50449400-50450600	Bivalent Enhancer	Fetal Stomach	stomach
40	chr12:50449400-50450600	Bivalent Enhancer	Stomach Mucosa	stomach
41	chr12:50449400-50450800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr12:50449400-50450800	Bivalent Enhancer	Fetal Lung	lung

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